Specter of Konoha
by Frostfyre Fox
Summary: Naruto endeavors to ascend through the ninja world with a focus on stealth and assassination, the true paradigm of a ninja after being apprenticed to Jiraiya. As his journey continues Naruto stumbles upon many secrets long hidden and brings them to light, all while the world around him starts to notice exactly who he is.
1. Chapter 1

**A/N: Sorry for such a long delay on getting this reuploaded. It took a long time for me to get my life in a larger semblance of order. My profile has the important updates of both my life and my plans for stories. This isn't going to go past the time skip and will eventually continue with a full sequel. In addition this story will NOT be canon, so do not get overly upset if things don't go the way of canon or certain characters/events don't get the screen time you think they deserve.**

**In addition I will be using English names of locations and technique names following the _ Release: _ Technique format. So if that's a turn off for you then you're more than welcome to leave because it's not going to change.**

**One Time Disclaimer: I do not own Naruto.**

* * *

Things had changed in the Village Hidden in the Leaves, ever since the induction of the fourth hokage, Minato Namikaze, the training of the village's shinobi had changed. The concession to this ramped up program that would bolster the forces was that the civilians would be granted some form of power, however the young hokage was smarter than the elders or the power-hungry civilian leaders had given him credit for and the position that was granted after the program was in place was essentially a figurehead position that was similar to the hokage but had command of solely civilian affairs, and who ultimately had to bend to the whims of the military leader that resided above them.

This maneuver had put Minato Namikaze into the elders' sights as a political power, even if he was the youngest leader the village had ever had the boy had a head for the political game and managed to get the changes he wanted without giving up anything and still keeping the public pleased, a delicate balance to strike and one that many leaders struggled with originally. But once more, the climate of the political game changed with an event far less human in nature nearly sixteen years prior.

From a hellish vortex came the beast, an ancient calamity, almost forgotten by the denizens of the stalwart village, the Nine-Tailed Fox appeared within the village and with no pause began to lay waste to the village's inhabitants, civilian and shinobi alike. As the body count rose, in what seemed to be everyone's darkest hour, a golden flash heralded the arrival of their salvation, the fourth hokage appeared on the beast's maw, and with another golden flash, the village was free of the beast's presence, but the battle was not over. As troops mobilized to the now distant but unfathomable beacon of chakra in the distance, the people knew not what their beloved leader was preparing to save their lives.

Arrays of seals, ancient and archaic in appearance and thrumming with the combined chakra of both Minato Namikaze and his wife Kushina Uzumaki, the final hope for the village rested amidst these runes, wailing in hunger, as newborns were oft to do. Naruto Uzumaki was the name he was granted upon his entrance into the world, his hair, though sparse could already be seen to take after both his parents, tufts sprouting up already in random locations, giving a glimpse of the spiked mane that would eventually frame the young boy's head while his mother's crimson tint painted it into a perfect union of his parents. Kushina lay next to her son, the life slowly draining from her due to the intense chakra use happening so soon after the laborious task of both birthing her son and subsequently having her prisoner ripped from her core by an assailant long since fled from the scene.

Minato and Kushina locked eyes once before nodding, the silent communication more than enough to let the other know it was time, as chakra erupted from their beings as all eight celestial gates were instantly torn open for the chakra they needed, and the life they had already forfeited.

With a flurry of chakra chains, hand seals and a tear filled farewell to their son, Kushina and Minato passed from the world, falling protectively around their child as he wailed to the world, a freshly emblazoned seal glowing into the night as the third hokage arrived. With a heavy heart and a subtle signal Hiruzen Sarutobi began his trek back to the village with the child as both Kushina and Minato's bodies were engulfed in flames, their secrets falling into the ashes their bodies would become.

Upon entering the village, the former leader announced the death of his successor and, now, predecessor as he reclaimed the mantle previously yielded before silently and with the skill of one of his caliber inducted Naruto into the registry of births in the past month, and hiding him away with the now orphaned newborns of the village. When questioned on the defeat of the cataclysmic beast, Hiruzen claimed pure ignorance, citing that he neither had an idea on how one would defeat the tailed beasts nor how one would even go about sealing away one as massive as the nine-tailed fox without prior preparation. The village unquestioningly believed their leader and simply believed their beloved fourth hokage had done the impossible as he had in the third shinobi war and simply found a solution to a problem no one else had even been contemplating. After all, a man who could single-handedly slaughter an army could surely seal away an entity like the fox, at least in their minds.

-=-=-=-=-=-=-=-= Time Skip: Graduation Day – 16 Years After Attack =-=-=-=-=-=-=-=-

The academy within the Hidden Leaf had always been lax in its training measures, even after the horrors of the warring clans, Hashirama and Madara could not bring themselves to train children to commit the same atrocities they themselves had been forced to do. The result was a watered down training routine heavily over emphasizing rhetoric and propaganda to endear the students to their nation instead of preparing them to defend it. This was a surprising success, despite the number of deaths and substantially weakened shinobi, the unity of the children under the teaching of 'The Will of Fire' oftentimes made up for the superior strength of their adversaries. This unfortunately perpetuated the system, which showed its flaws as other shinobi nations cropped up and the Hidden Leaf was no longer the only village employing cells of different clans of shinobi who were trained to work as a team. Despite this fact, the near cult-level worship of 'The Will of Fire' prevented any change from being made, until the fourth hokage.

The academy, which used to consist of a five year general training course from the ages of seven to twelve had been completely scrapped, instead adopting a full decade of training, starting a year earlier and extending to the age of sixteen, this allowed the students to get through the hormonal cocktail of puberty off the field while also enabling more specialized training to occur in order to boost the effectiveness of the students overall. The final year especially was important due to the reassignment of all E-Rank missions (what had previously been classified as D-Rank Domestic missions) to the students who were randomly assigned a different cell of 2 other students to form a real sense of camaraderie to their peers, instead of an ideal as well as to engender an understanding of their peer group's skill sets.

Naruto Uzumaki however, had not been amongst his peers for over three years though. In fact, today, on the day of graduation would be the first time he would actually meet any of his peers again after the years he had just vanished. Though to be fair, he wasn't really alone, the spy master of the leaf, Jiraiya had taken an interest in the boy due to his stealth and skills in espionage tactics and abilities, and as such had formally apprenticed the boy for the final three years of his academy stint, a rare but no less respectable turn of events. In the three years the boy had been drilled in stealth, reconnaissance and tactical espionage all while setting up contacts for his own spy network while being taken around the world with the toad summoning sage.

'_It's odd now that I think about it,_' Naruto mused to himself as he slipped into an empty seat in the back of the room, only being noticed by Shino Aburame and Hinata Hyuga, '_how a man as noticeable as Jiraiya can blend into any crowd so easily and despite his reputation as a powerful shinobi effectively disarm any worries about his ability with such a simple quirk. 'Super pervert' my ass, the man might have an overt attraction to the opposite sex but anyone with a brain can tell it's mostly an act._'

Naruto had grown well under Jiraiya's watchful eye, learning observation and seal work, though his main skills were all at their most effective with his high levels of stealth. It hadn't taken Naruto long to realize the man had a great deal to teach him on stealth when he regularly seemed to appear next to the boy without so much as an iota of chakra use despite his impressive frame of over six foot and rather muscled build; in fact, had Naruto seen him and only known of his reputation prior to facing Jiraiya, he would have assumed the man to be a nin/taijutsu user and not an assassin and spymaster.

While Jiraiya's choice of disarming quirk hadn't bled into Naruto's persona that he had crafted something a bit more humorous, to him at least, had cropped up in its place, and had saved his life a few times during his training by completely lowering the guards of his enemies. Despite all the changes it wasn't unheard of for cannon fodder to still make it through the academy program as just that, and so Naruto decided to play up that fact when he got into combat, making himself out to be a support shinobi who was better as a tactician off the field; a tremble here and there, a misstep calculated enough to make it believable but still give him ground and most trained and even untrained shinobi would begin to write him off. A trip and "misaimed" kunai or two and their guards would drop enough to only realize they were dead when his kunai buried itself in their neck.

'_Deception and misinformation are your greatest allies and most dangerous foes Naruto; never forget that your actions embody the very thing you could be facing at any moment. If an opponent gives you any opening you give them a kunai; you can never be sure if they're not working the same angle as you and at the very least if they block you can abandon all pretense and show them the skills that will make you a legend._'

The words of his teacher echoed in his mind as he glanced around the room and saw the clan heirs, unassuming overall and initially a disappointment to him until that gem of wisdom resurfaced. With a more concentrated focus he looked again and saw a single heir that would have killed him had he been an enemy and even having a single rival in his craft excited Naruto, even more so when the Nara heir lazily mouthed the word that would spark a great friendship.

'Dead'

As Naruto nodded, giving the shadow wielder his win, Iruka cleared his throat and looked around the room, his eyes locking with Naruto's for a brief moment before nodding slightly and addressing the class.

"You have made it through your training and will now be assigned to teams in order to further your training and prepare you for the world beyond our barriers and walls. Let's begin, the following teams will be yours until you all either reach Chunin or shake hands with the reaper, so make sure you understand the bonds you craft with them."

As Iruka took a slight break to let his words sink in he took in the expression of his students.

'_Watch out world…the next generation of the Hidden Leaf is going to take you by storm._'


	2. Chapter 2

**A/N: So I have already failed my promise, though mostly due to my cable company doing the same to me. I was given the impression that when I moved on the first of the month that both my internet and my electricity would be able to come with me, unfortunately Charter was a dirty, stinking liar and I still don't have internet until Saturday when Time Warner hooks me up (that said I got lucky in NOT signing up for another 12 month contract with Charter so there's at least a small mercy). That said, I've got a third chapter on my flash drive and will upload it tomorrow or Friday while hopefully getting both of the first chapters of Jupiter's Maelstrom uploaded by Friday; since I'm only able to do this during breaks at work I'm not sure I can guarantee they'll be uploaded before Saturday but I'll do my best. That said here's chapter two and I hope you enjoy it.**

**Quick Responses to a couple reviews though, since I'm not completely oblivious to them (and a forewarning that even if the response comes across as chastising it is being delivered with the internet equivalent of a 'statement voice', as though I was telling you that the weather today, despite being cold as balls for most of my working peers is my favorite kind of weather).**

**RedEye00 - I'm glad you noticed that, and that is indeed the point. The other genin won't be properly introduced except in bits and pieces as they come into direct contact with Naruto in some way or form. This is going to fit a lot of further actions as well as you won't really get details until a character reveals them if Naruto wouldn't necessarily know them, and as the reader you might not even know what Naruto knows unless you pay attention to the details that are sometimes going to be hidden in dialogue and actions.**

**Milton - While I appreciate your forethought on the topic and the fact that not only are you willing to attempt to go through my story despite it not being your preferred pairing, I do want to point out that as the author (and a huge fan of NaruHina myself) that I'm not changing the pairing (at all, no harem either for people who are into suggesting that sort of thing) but I am listening to your suggestions. I was already thinking of doing either NaruIno or NaruTen for my Golden Sun/Naruto xover and I'm really leaning towards a romance aspect where he goes through the motions with both of them before seeing the audience's feel on either before settling on the pairing exactly.**

**I do not own Naruto or any of the likenesses that appear as Naruto's various masks, they all belong to their respective owners and I am making zero monies off of this work of pure fiction.**

**Please Read & Review!**

* * *

Footsteps echoed through the room, wood hitting stone in a slow pattern, indicating the slow gait of the newest entrant into the bar located precisely between the red-light district and the 'clean' section of the Hidden Leaf village. The figure was rather imposing, garbed in traditional samurai attire dyed a peculiar, metallic red, and a sword on the man's waist. His steps and bearing showed an experience with the blade that made any of the typical thieves at the infamous "Twilight Bar" back away from the figure lest they lose a hand.

Despite his rather imposing presence a single child ran to the man, bumping into him before bolting, seeming to never alert the man to the missing documents on his person. In what another thief expected to be a smooth move he "valiantly" pointed the running child out to the man.

"Tha' little shit jus' ran off with somethin' of yours!"

The samurai glanced up to the man, his red eyes and cross scar under his right eye giving him a very memorable appearance.

"I assure you sir, that if the child had stolen anything I would have stopped him before he got more than a few feet away, that I would have."

The man grit his teeth, having sworn he had seen the kid pocket something, and so in an attempt to make a pass at a seemingly proud but easy mark the man brushed past the samurai, pocketing a small pull of coins. He hadn't made it a full step past the samurai before the sheathed katana at the samurai's waist found its way to the back of his head.

"I believe I made my point clear on his theft, though I didn't think you would be so stupid as to test my claim, that I did not."

The thief's eyes widened in fear, especially when he realized his mark had not only noticed and stopped his escape but had already retrieved his stolen goods in the time it took him to make that simple declaration. With a slight whimper the man vanished into the shadows, afraid for his life. Walking to the bar he looked to the bartender and gave a small, reserved smile.

"Firewater Sake from Tanzaku."

The bartender passed the drink to the samurai and went back to his work, even as the goliath of a shinobi sat next to the samurai.

"You're good samurai. Interesting choice of sword for one such as yourself; given that it's being worn like that I would assume you've a reverse-edge blade."

The samurai glanced over to the near legendary shinobi that had sat next to him, recognizing him by both his impressive frame and the iconic 'Oil' marked headband that sat atop his brow as Jiraiya the toad sage.

"If I recall correctly Master Jiraiya, we met once before at Tanzaku where you chose to ignore the plight of a young child simply due to your…preoccupation with the street worker who called herself Ginger, that you did."

Though the samurai's expression never shifted the tone the statement was delivered in left no mistake what the warrior's impression of the sage was. With a slight grimace Jiraiya stood up, and noted the now empty cup of sake in front of the samurai before laying down the price of the drink to the barkeep.

"Come on, we need to get you to see the Hokage, it's why I'm here in the first place."

The samurai narrowed his eyes before nodding once and walking alongside the legendary shinobi before both seemed to vanish in two very different high speed techniques, only to appear in an old run down apartment far beyond the traveled path for anyone who wasn't informed of its existence.

"So, I got the files kid, what do you think of the teams?"

The samurai went up in a puff of smoke, leaving Naruto standing there, his red hair currently styled far more in his mother's style than anything his father had ever worn, giving him an almost effeminate look, one that he simultaneously cursed and was happy for due to the instant underestimation it netted him even before he began acting.

"Standard stuff old man, the 'face' with the familiar line up of Chouji, Ino, and Shikamaru a full frontal assault team with Sasuke, Sakura and Sai and let's not forget the capture, tracking and interrogation team with Hinata, Kiba and Shino. Honestly the teams are perfectly lined up for what they needed them to do. Surprised at the amount of prospects heading to the general corps though, normally they get the scraps."

Jiraiya watched the boy and nodded once, "You're starting to read into the right things kid. We've got whispers of war on the horizon and while the team setup is great for our 'public' shinobi we have to make sure we're properly 'staffed' with defenders and saboteurs in case of emergency. After we cleansed that leak that used to be called Kabuto we've been able to keep a much tighter hold on the information our enemies are fed and they're afraid of that. I do have to know though, how did you convince the old man to let you use his grandson for covert ops?"

Naruto smiled, unsurprised that his teacher had seen through Konohamaru's disguise, "The kid is dying for attention and that'll get him killed. The both of us figured it'd help him get through life if he was unofficially apprenticed to me, show him that the spotlight is the opposite of what he wants. Unlike me though, since he'll get to be part of the 'face' of our village, no one would ever suspect he WAS a black ops agent even if they managed to see through his display. After all, why would we send out such an influential player's family without some form of serious insurance policy?"

Jiraiya laughed outright at that and noted the point. He affixed Naruto with a serious look before passing him a small scroll and adopting his serious demeanor that accompanied his mission briefings.

"You've got a live one who'll likely use the west woods as an exit point. Target is a Chunin instructor, Mizuki, I'm sure you've met him. Got in contact with Orochimaru years ago, thought he got out from the radar when we _dispatched_ Kabuto and left him be, but now he's got plans to get away with the forbidden scroll. Take him out, return the scroll, and the old man says if you do it before he has to raise the alarm than he's got a surprise of some kind for you."

Jiraiya stared at his apprentice and watched him nod before incinerating the scroll and vanishing from the spot before the ashes hit the ground.

"You're getting there kid…keep at it."

Anyone who had been in the room would have felt they had heard a ghost seeing as how Jiraiya too had vanished even before the words had fully been formed, an eerie effect master and apprentice had mastered for their stealth techniques, giving them the apt moniker of specters.

Mizuki ran, and he ran fast; he wasn't sure how he managed to escape the pruning of Orochimaru's men that had happened a year ago but he was beyond himself that he had somehow escaped. Despite this, he knew he had to bide his time before he made his escape, and a year after the pruning, when he was sure the village had definitely forgotten about the whole debacle. Despite his self assurance, Mizuki never broke stride, even when he reached the forest, well beyond the normal patrol routes of the village. It was only due to his paranoia that he managed to dodge the strange kunai affixed with an 'S' along the blade.

"Chunin Mizuki, you are sentenced to death for your theft of the forbidden scroll of seals, prepare yourself!"

A feminine voice sounded, alerting Mizuki to a woman with red hair, leather garb that was really designed for mobility more than protection who was not only equipped with a salvo's worth of daggers and kunai all shaped with the 'S' along the blade but who was charging at him before she seemed to vanish before his eyes and he felt a sudden pain, and then nothing.

Before Mizuki's body even his the ground Naruto, henged in the form he referred to as 'Katarina' had picked up the scroll and vanished, his use of chakra to dispatch Mizuki being the beacon that alerted the ANBU to the corpse's location.

The kunai lodged firmly in the Chunin's neck would be the only clue the ANBU managed to salvage to identify the attacker, though no culprit would ever be found outside a rumor milling about the village of a vigilante going by the moniker 'the Sinister Blade'.

As Naruto materialized in the Hokage's library he idly noted the bizarre lack of guards despite the recent theft of such a high value scroll. With a roll of his eyes at the rather lax security measures the village employed due to its top-dog status, Naruto replaced the scroll before utilizing his and Jiraiya's unique shunshin to appear in front of the Hokage's office. With a swift three knocks the grizzled voice of his leader sounded through the door.

"Come in Naruto, we have much to discuss."

The young shinobi walked in before closing the door behind him, shrouding the room from outside observance even as the blue thrum of chakra empowered seals bathed the room in their light before the leader leaned forward, his expression almost critical of the boy in front of him.

"You've returned the scroll I assume, I'll need a full report, especially on the location of…certain documents that appear to have gone missing from the academy's archives."

Naruto nodded once before giving him a full rundown of his capture mission, including the complete transformation into Katarina and his lack of shock or joy at seeing the incredibly lax security even after such a high profile theft.

"As for the documents you're talking about, I'm not sure what I could tell you. I've not been in the academy since my examination and unless you're implying I was capable of getting both into and out of the archives without being detected while simultaneously performing my examination, I would have to ask you how I would have accomplished this without being caught by any of the guards that would have to be stationed there."

Hiruzen let a small, nigh unnoticeable smirk onto his face before it vanished, too fast for any shinobi below his caliber (which was admittedly a list of all but about four shinobi left alive in the world) would be able to notice. He settled his face into a contemplative grimace as he gazed at the apprentice to the best spymaster he had ever seen within the village and really attempted to weigh the pros and cons of the various boons he had to choose from to grant the boy to keep his agreement to his master.

"Naruto, in your apartment, or at least by the time you get there, will be a scroll that's keyed into your mother's blood. The contents are, for obvious reasons, dangerous to talk about directly given her status as the princess of the now defunct Uzumaki clan, since it's absolutely pointless to have the scroll without both your fresh blood AND your rather…unique chakra, the scroll has been held until you would prove yourself ready to truly begin your studies into sealing. While one could argue that you were ready technically there still stood the need to prove your loyalty to the powers the village you find yourself in; at least by law. Know that I had every faith that you would pass but had my hands tied by the Daiymo in this regard, in any case I expect you to have at least finished the first scroll within the week and return to me with further instructions on the dissemination of your Uzumaki Inheritance as the scroll dictates. Are we clear Genin Uzumaki?"

The dismissal in his voice was both audible and unnecessary given the command, as lacking in direct verbage as it was, was still abundantly clear in the last statement. With a curt nod and a vanishing frame the boy's voice echoed along the walls in a way that reminded Sarutobi of his only remaining loyal student.

"As you command, Lord Hokage."

The elderly leader gazed pensively out towards his village as the acrid, yet sweet tasting smoke began to fill more of his office and a wry smile worked its way onto his aged face, a clone appearing smokeless, seallessly, and noiselessly before assisting him in the sorting of the various reports to be distributed amongst his top Jonin for review and cataloguing. After all, being the supreme military leader of a village of highly trained assassins meant he had to have time to train lest a sudden yet inevitable coup succeeded in taking his life; he didn't get this old sitting behind a desk all day after all.

'_The Elemental Nations are going to be changed forever by that boy Jiraiya…I can only hope we survive the sundering he is sure to leave in his wake._'

With a final shuffle of papers and a vanishing clone the aged leader leapt out the window towards his private training ground, once more drilling himself through decades worth of fighting stances and techniques, making sure his form was in top condition, especially if the word Jiraiya brought was true.


End file.
